A sensitive semi-nested reverse transcriptase-polymerase chain reaction (RT-PCR) amplification was performed to evaluate estrogen receptor-alpha (ER-alpha) mRNA expression in prostate cancer cell lines. We demonstrated the presence of wild-type ER-alpha (wt ER-alpha) and five ER-alpha variants, designated ER-alphaA, B, C, D, and E. Unlike ER-alphaA and D, ER-alphaB, C, and E were not previously reported in normal or cancerous mammalian cells. DNA sequencing analysis of these ER-alpha variants revealed the genetic changes to be either in-frame or out-of-frame deletions. The expression of each ER-alpha variant differs significantly depending on the androgen responsiveness, tumorigenic and metastatic potentials of each prostate cancer cell line. The potential functional significance of ER-alpha variants was assessed in yeast two-hybrid and ERE promoter-reporter mammalian transcription assay systems. The results of these studies indicated that none of the ER-alpha variants can form homo- or heterodimers either with wt ER-alpha or among themselves in vivo, and that these ER-alpha variants have no demonstrable transcriptional or dominant-negative activity, as assessed in vitro.